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Example 31 with RelatedArtifact

use of org.hl7.fhir.r4b.model.RelatedArtifact in project cqf-ruler by DBCG.

the class ActivityDefinitionApplyProvider method resolveTask.

private Task resolveTask(ActivityDefinition activityDefinition, String patientId) {
    Task task = new Task();
    task.setStatus(Task.TaskStatus.DRAFT);
    task.setIntent(Task.TaskIntent.PROPOSAL);
    task.setFor(new Reference(patientId));
    Task.ParameterComponent input = new Task.ParameterComponent();
    if (activityDefinition.hasCode()) {
        task.setCode(activityDefinition.getCode());
        input.setType(activityDefinition.getCode());
    }
    // Extension defined by CPG-on-FHIR for Questionnaire canonical URI
    Extension collectsWith = activityDefinition.getExtensionByUrl("http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-collectWith");
    if (collectsWith != null && collectsWith.getValueAsPrimitive().toString() != null) {
        CanonicalType uri = new CanonicalType(collectsWith.getValueAsPrimitive().toString());
        input.setValue(uri);
    }
    if (activityDefinition.hasRelatedArtifact()) {
        for (RelatedArtifact artifact : activityDefinition.getRelatedArtifact()) {
            if (artifact.hasUrl()) {
                Attachment attachment = new Attachment().setUrl(artifact.getUrl());
                if (artifact.hasDisplay()) {
                    attachment.setTitle(artifact.getDisplay());
                }
                input.setValue(artifact.hasDisplay() ? attachment.setTitle(artifact.getDisplay()) : attachment);
            }
        // TODO - other relatedArtifact types
        }
    }
    // If input has been populated, then add it to the Task.
    if (input.getType() != null || input.getValue() != null) {
        task.addInput(input);
    }
    return task;
}
Also used : Extension(org.hl7.fhir.r4.model.Extension) Task(org.hl7.fhir.r4.model.Task) Reference(org.hl7.fhir.r4.model.Reference) Attachment(org.hl7.fhir.r4.model.Attachment) RelatedArtifact(org.hl7.fhir.r4.model.RelatedArtifact) CanonicalType(org.hl7.fhir.r4.model.CanonicalType)

Example 32 with RelatedArtifact

use of org.hl7.fhir.r4b.model.RelatedArtifact in project cqf-ruler by DBCG.

the class Session method resolveCdsHooksPlanDefinition.

// For library use
public CarePlan resolveCdsHooksPlanDefinition(Context context, PlanDefinition planDefinition, String patientId, RequestDetails theRequest) {
    CarePlanBuilder carePlanBuilder = new CarePlanBuilder();
    RequestGroupBuilder requestGroupBuilder = new RequestGroupBuilder().buildStatus().buildIntent();
    // links
    if (planDefinition.hasRelatedArtifact()) {
        List<Extension> extensions = new ArrayList<>();
        for (RelatedArtifact relatedArtifact : planDefinition.getRelatedArtifact()) {
            AttachmentBuilder attachmentBuilder = new AttachmentBuilder();
            ExtensionBuilder extensionBuilder = new ExtensionBuilder();
            if (relatedArtifact.hasDisplay()) {
                // label
                attachmentBuilder.buildTitle(relatedArtifact.getDisplay());
            }
            if (relatedArtifact.hasUrl()) {
                // url
                attachmentBuilder.buildUrl(relatedArtifact.getUrl());
            }
            if (relatedArtifact.hasExtension()) {
                // type
                attachmentBuilder.buildExtension(relatedArtifact.getExtension());
            }
            extensionBuilder.buildUrl("http://example.org");
            extensionBuilder.buildValue(attachmentBuilder.build());
            extensions.add(extensionBuilder.build());
        }
        requestGroupBuilder.buildExtension(extensions);
    }
    resolveActions(planDefinition.getAction(), context, patientId, requestGroupBuilder, new ArrayList<>(), theRequest);
    CarePlanActivityBuilder carePlanActivityBuilder = new CarePlanActivityBuilder();
    carePlanActivityBuilder.buildReferenceTarget(requestGroupBuilder.build());
    carePlanBuilder.buildActivity(carePlanActivityBuilder.build());
    return carePlanBuilder.build();
}
Also used : Extension(org.hl7.fhir.r4.model.Extension) AttachmentBuilder(org.opencds.cqf.ruler.cr.r4.builder.AttachmentBuilder) CarePlanBuilder(org.opencds.cqf.ruler.cr.r4.builder.CarePlanBuilder) RequestGroupBuilder(org.opencds.cqf.ruler.cr.r4.builder.RequestGroupBuilder) ArrayList(java.util.ArrayList) ExtensionBuilder(org.opencds.cqf.ruler.cr.r4.builder.ExtensionBuilder) RelatedArtifact(org.hl7.fhir.r4.model.RelatedArtifact) CarePlanActivityBuilder(org.opencds.cqf.ruler.cr.r4.builder.CarePlanActivityBuilder)

Example 33 with RelatedArtifact

use of org.hl7.fhir.r4b.model.RelatedArtifact in project cqf-ruler by DBCG.

the class STU3CarePlanToCdsCard method convert.

private static List<CdsCard> convert(RequestGroup requestGroup) {
    List<CdsCard> cards = new ArrayList<>();
    // links
    List<CdsCard.Links> links = new ArrayList<>();
    if (requestGroup.hasExtension()) {
        for (Extension extension : requestGroup.getExtension()) {
            CdsCard.Links link = new CdsCard.Links();
            if (extension.getValue() instanceof Attachment) {
                Attachment attachment = (Attachment) extension.getValue();
                if (attachment.hasUrl()) {
                    link.setUrl(attachment.getUrl());
                }
                if (attachment.hasTitle()) {
                    link.setLabel(attachment.getTitle());
                }
                if (attachment.hasExtension()) {
                    link.setType(attachment.getExtensionFirstRep().getValue().primitiveValue());
                }
            } else {
                throw new RuntimeException("Invalid link extension type: " + extension.getValue().fhirType());
            }
            links.add(link);
        }
    }
    if (requestGroup.hasAction()) {
        for (RequestGroup.RequestGroupActionComponent action : requestGroup.getAction()) {
            IParser jsonParser = FhirContext.forCached(FhirVersionEnum.DSTU3).newJsonParser().setPrettyPrint(true);
            CdsCard card = new CdsCard(jsonParser);
            // basic
            if (action.hasTitle()) {
                card.setSummary(action.getTitle());
            }
            if (action.hasDescription()) {
                card.setDetail(action.getDescription());
            }
            if (action.hasExtension()) {
                card.setIndicator(action.getExtensionFirstRep().getValue().toString());
            }
            // source
            if (action.hasDocumentation()) {
                // Assuming first related artifact has everything
                RelatedArtifact documentation = action.getDocumentationFirstRep();
                CdsCard.Source source = new CdsCard.Source();
                if (documentation.hasDisplay()) {
                    source.setLabel(documentation.getDisplay());
                }
                if (documentation.hasUrl()) {
                    source.setUrl(documentation.getUrl());
                }
                if (documentation.hasDocument() && documentation.getDocument().hasUrl()) {
                    source.setIcon(documentation.getDocument().getUrl());
                }
                card.setSource(source);
            }
            if (action.hasSelectionBehavior()) {
                card.setSelectionBehavior(action.getSelectionBehavior().toCode());
            }
            // suggestions
            // TODO - uuid
            boolean hasSuggestions = false;
            CdsCard.Suggestions suggestions = new CdsCard.Suggestions();
            CdsCard.Suggestions.Action actions = new CdsCard.Suggestions.Action();
            if (action.hasLabel()) {
                suggestions.setLabel(action.getLabel());
                hasSuggestions = true;
                if (action.hasDescription()) {
                    actions.setDescription(action.getDescription());
                }
                if (action.hasType() && !action.getType().getCode().equals("fire-event")) {
                    String code = action.getType().getCode();
                    actions.setType(CdsCard.Suggestions.Action.ActionType.valueOf(code.equals("remove") ? "delete" : code));
                }
                if (action.hasResource()) {
                    if (actions.getType().name().equalsIgnoreCase("create")) {
                        action.getResourceTarget().setId((String) null);
                    }
                    actions.setResource(action.getResourceTarget());
                }
            }
            if (hasSuggestions) {
                suggestions.addAction(actions);
                card.addSuggestion(suggestions);
            }
            if (!links.isEmpty()) {
                card.setLinks(links);
            }
            cards.add(card);
        }
    }
    return cards;
}
Also used : ArrayList(java.util.ArrayList) Attachment(org.hl7.fhir.dstu3.model.Attachment) RelatedArtifact(org.hl7.fhir.dstu3.model.RelatedArtifact) Extension(org.hl7.fhir.dstu3.model.Extension) RequestGroup(org.hl7.fhir.dstu3.model.RequestGroup) IParser(ca.uhn.fhir.parser.IParser)

Example 34 with RelatedArtifact

use of org.hl7.fhir.r4b.model.RelatedArtifact in project quality-measure-and-cohort-service by Alvearie.

the class CohortCLITest method testMainFHIRLibrariesWithDependencies.

@Test
public void testMainFHIRLibrariesWithDependencies() throws Exception {
    FhirServerConfig fhirConfig = getFhirServerConfig();
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", Enumerations.AdministrativeGender.FEMALE, "1978-05-06");
    mockFhirResourceRetrieval(patient);
    Library root = getLibrary("Breast-Cancer-Screening", DEFAULT_RESOURCE_VERSION, "cql/includes/Breast-Cancer-Screening.cql");
    Library helpers = getLibrary("FHIRHelpers", "4.0.0", "cql/fhir-helpers/FHIRHelpers.cql", "text/cql", "cql/fhir-helpers/FHIRHelpers.xml", "application/elm+json");
    RelatedArtifact related = new RelatedArtifact();
    related.setType(RelatedArtifactType.DEPENDSON);
    related.setResource("/Library/" + helpers.getId());
    root.addRelatedArtifact(related);
    mockFhirResourceRetrieval(root);
    mockFhirSingletonBundleRetrieval(helpers);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(fhirConfig));
    }
    try {
        PrintStream originalOut = System.out;
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        try (PrintStream captureOut = new PrintStream(baos)) {
            System.setOut(captureOut);
            CohortCLI.main(new String[] { "-d", tmpFile.getAbsolutePath(), "-f", root.getId(), "-l", root.getName(), "-v", root.getVersion(), "-c", patient.getId(), "-s", "CQL" });
        } finally {
            System.setOut(originalOut);
        }
        String output = new String(baos.toByteArray());
        String[] lines = output.split("\r?\n");
        assertEquals(output, 12, lines.length);
        System.out.println(output);
        verify(1, getRequestedFor(urlEqualTo("/Patient/" + patient.getId() + "?_format=json")));
        verify(1, getRequestedFor(urlEqualTo("/Library/" + root.getId() + "?_format=json")));
    } finally {
        tmpFile.delete();
    }
}
Also used : PrintStream(java.io.PrintStream) FileWriter(java.io.FileWriter) Patient(org.hl7.fhir.r4.model.Patient) FhirServerConfig(com.ibm.cohort.fhir.client.config.FhirServerConfig) Library(org.hl7.fhir.r4.model.Library) ByteArrayOutputStream(java.io.ByteArrayOutputStream) RelatedArtifact(org.hl7.fhir.r4.model.RelatedArtifact) File(java.io.File) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) FileWriter(java.io.FileWriter) Writer(java.io.Writer) Test(org.junit.Test)

Example 35 with RelatedArtifact

use of org.hl7.fhir.r4b.model.RelatedArtifact in project quality-measure-and-cohort-service by Alvearie.

the class R4LibraryDependencyGatherer method recurse.

private List<Library> recurse(Library library, Set<String> loadedCanonicalUrls) {
    String canonicalUrl = CanonicalHelper.toCanonicalUrl(library.getUrl(), library.getVersion());
    if (loadedCanonicalUrls.contains(canonicalUrl)) {
        return Collections.emptyList();
    }
    List<Library> retVal = new ArrayList<>();
    retVal.add(library);
    loadedCanonicalUrls.add(canonicalUrl);
    if (library.hasRelatedArtifact()) {
        for (RelatedArtifact related : library.getRelatedArtifact()) {
            if (related.hasType() && related.getType().equals(RelatedArtifact.RelatedArtifactType.DEPENDSON) && related.hasResource()) {
                String relatedIdentifier = related.getResource();
                Library relatedLibrary = resolveLibrary(relatedIdentifier);
                if (relatedLibrary != null) {
                    retVal.addAll(recurse(relatedLibrary, loadedCanonicalUrls));
                }
            }
        }
    }
    return retVal;
}
Also used : ArrayList(java.util.ArrayList) Library(org.hl7.fhir.r4.model.Library) RelatedArtifact(org.hl7.fhir.r4.model.RelatedArtifact)

Aggregations

RelatedArtifact (org.hl7.fhir.r4.model.RelatedArtifact)13 Complex (org.hl7.fhir.r4.utils.formats.Turtle.Complex)13 ArrayList (java.util.ArrayList)7 Complex (org.hl7.fhir.dstu3.utils.formats.Turtle.Complex)7 RelatedArtifact (org.hl7.fhir.dstu3.model.RelatedArtifact)6 XhtmlNode (org.hl7.fhir.utilities.xhtml.XhtmlNode)6 Attachment (org.hl7.fhir.r4.model.Attachment)5 IParser (ca.uhn.fhir.parser.IParser)4 Extension (org.hl7.fhir.r4.model.Extension)4 Library (org.hl7.fhir.r4.model.Library)4 RelatedArtifact (org.hl7.fhir.r5.model.RelatedArtifact)4 Attachment (org.hl7.fhir.dstu3.model.Attachment)3 Reference (org.hl7.fhir.r4.model.Reference)3 FhirContext (ca.uhn.fhir.context.FhirContext)2 IdDt (ca.uhn.fhir.model.primitive.IdDt)2 ObjectMapper (com.fasterxml.jackson.databind.ObjectMapper)2 FhirServerConfig (com.ibm.cohort.fhir.client.config.FhirServerConfig)2 ByteArrayOutputStream (java.io.ByteArrayOutputStream)2 File (java.io.File)2 FileWriter (java.io.FileWriter)2